Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Amine GHOZLANE
shaman
Commits
663d1592
Commit
663d1592
authored
Sep 18, 2019
by
Amine GHOZLANE
Browse files
Force expended model
parent
e676c88e
Pipeline
#14734
canceled with stages
in 42 minutes and 34 seconds
Changes
2
Pipelines
1
Show whitespace changes
Inline
Side-by-side
Rfunctions/Stat_Model.R
View file @
663d1592
...
...
@@ -63,14 +63,14 @@ Get_dds_object <- function(input,counts,target,design,normFactorsOTU,CT_noNorm,C
# dds <- nbinomWaldTest(dds,modelMatrixType = "expanded")
if
(
nrow
(
counts
)
*
nrow
(
target
)
>=
50000
)
{
dds
=
DESeq2shaman
::
DESeq
(
dds
,
fitType
=
input
$
fitType
,
parallel
=
TRUE
,
minReplicatesForReplace
=
Inf
)
dds
=
DESeq2shaman
::
DESeq
(
dds
,
fitType
=
input
$
fitType
,
parallel
=
TRUE
,
minReplicatesForReplace
=
Inf
,
modelMatrixType
=
"expanded"
)
# try(DESeq(dds,fitType=input$fitType,parallel = TRUE,minReplicatesForReplace = Inf) ->ddstmp,silent = TRUE)
# if(!is.null(ddstmp)) dds = ddstmp
}
if
(
nrow
(
counts
)
*
nrow
(
target
)
<
50000
||
is.null
(
dds
))
{
dds
<-
DESeq2shaman
::
estimateDispersions
(
dds
,
fitType
=
input
$
fitType
)
dds
<-
DESeq2shaman
::
nbinomWaldTest
(
dds
)
dds
<-
DESeq2shaman
::
nbinomWaldTest
(
dds
,
modelMatrixType
=
"expanded"
)
}
# dds <- DESeq(dds,fitType=input$fitType,modelMatrixType = "expanded",parallel = TRUE)
# }
...
...
www/Workflow_sh.png
View replaced file @
e676c88e
View file @
663d1592
757 KB
|
W:
|
H:
644 KB
|
W:
|
H:
2-up
Swipe
Onion skin
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment